multipers 2.2.3__cp312-cp312-win_amd64.whl → 2.3.1__cp312-cp312-win_amd64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.


This version of multipers might be problematic. Click here for more details.

Files changed (182) hide show
  1. multipers/__init__.py +33 -31
  2. multipers/_signed_measure_meta.py +430 -430
  3. multipers/_slicer_meta.py +211 -212
  4. multipers/data/MOL2.py +458 -458
  5. multipers/data/UCR.py +18 -18
  6. multipers/data/graphs.py +466 -466
  7. multipers/data/immuno_regions.py +27 -27
  8. multipers/data/pytorch2simplextree.py +90 -90
  9. multipers/data/shape3d.py +101 -101
  10. multipers/data/synthetic.py +113 -111
  11. multipers/distances.py +198 -198
  12. multipers/filtration_conversions.pxd.tp +84 -84
  13. multipers/filtrations/__init__.py +18 -0
  14. multipers/{ml/convolutions.py → filtrations/density.py} +563 -520
  15. multipers/filtrations/filtrations.py +289 -0
  16. multipers/filtrations.pxd +224 -224
  17. multipers/function_rips.cp312-win_amd64.pyd +0 -0
  18. multipers/function_rips.pyx +105 -105
  19. multipers/grids.cp312-win_amd64.pyd +0 -0
  20. multipers/grids.pyx +350 -350
  21. multipers/gudhi/Persistence_slices_interface.h +132 -132
  22. multipers/gudhi/Simplex_tree_interface.h +239 -245
  23. multipers/gudhi/Simplex_tree_multi_interface.h +516 -561
  24. multipers/gudhi/cubical_to_boundary.h +59 -59
  25. multipers/gudhi/gudhi/Bitmap_cubical_complex.h +450 -450
  26. multipers/gudhi/gudhi/Bitmap_cubical_complex_base.h +1070 -1070
  27. multipers/gudhi/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +579 -579
  28. multipers/gudhi/gudhi/Debug_utils.h +45 -45
  29. multipers/gudhi/gudhi/Fields/Multi_field.h +484 -484
  30. multipers/gudhi/gudhi/Fields/Multi_field_operators.h +455 -455
  31. multipers/gudhi/gudhi/Fields/Multi_field_shared.h +450 -450
  32. multipers/gudhi/gudhi/Fields/Multi_field_small.h +531 -531
  33. multipers/gudhi/gudhi/Fields/Multi_field_small_operators.h +507 -507
  34. multipers/gudhi/gudhi/Fields/Multi_field_small_shared.h +531 -531
  35. multipers/gudhi/gudhi/Fields/Z2_field.h +355 -355
  36. multipers/gudhi/gudhi/Fields/Z2_field_operators.h +376 -376
  37. multipers/gudhi/gudhi/Fields/Zp_field.h +420 -420
  38. multipers/gudhi/gudhi/Fields/Zp_field_operators.h +400 -400
  39. multipers/gudhi/gudhi/Fields/Zp_field_shared.h +418 -418
  40. multipers/gudhi/gudhi/Flag_complex_edge_collapser.h +337 -337
  41. multipers/gudhi/gudhi/Matrix.h +2107 -2107
  42. multipers/gudhi/gudhi/Multi_critical_filtration.h +1038 -1038
  43. multipers/gudhi/gudhi/Multi_persistence/Box.h +171 -171
  44. multipers/gudhi/gudhi/Multi_persistence/Line.h +282 -282
  45. multipers/gudhi/gudhi/Off_reader.h +173 -173
  46. multipers/gudhi/gudhi/One_critical_filtration.h +1433 -1431
  47. multipers/gudhi/gudhi/Persistence_matrix/Base_matrix.h +769 -769
  48. multipers/gudhi/gudhi/Persistence_matrix/Base_matrix_with_column_compression.h +686 -686
  49. multipers/gudhi/gudhi/Persistence_matrix/Boundary_matrix.h +842 -842
  50. multipers/gudhi/gudhi/Persistence_matrix/Chain_matrix.h +1350 -1350
  51. multipers/gudhi/gudhi/Persistence_matrix/Id_to_index_overlay.h +1105 -1105
  52. multipers/gudhi/gudhi/Persistence_matrix/Position_to_index_overlay.h +859 -859
  53. multipers/gudhi/gudhi/Persistence_matrix/RU_matrix.h +910 -910
  54. multipers/gudhi/gudhi/Persistence_matrix/allocators/entry_constructors.h +139 -139
  55. multipers/gudhi/gudhi/Persistence_matrix/base_pairing.h +230 -230
  56. multipers/gudhi/gudhi/Persistence_matrix/base_swap.h +211 -211
  57. multipers/gudhi/gudhi/Persistence_matrix/boundary_cell_position_to_id_mapper.h +60 -60
  58. multipers/gudhi/gudhi/Persistence_matrix/boundary_face_position_to_id_mapper.h +60 -60
  59. multipers/gudhi/gudhi/Persistence_matrix/chain_pairing.h +136 -136
  60. multipers/gudhi/gudhi/Persistence_matrix/chain_rep_cycles.h +190 -190
  61. multipers/gudhi/gudhi/Persistence_matrix/chain_vine_swap.h +616 -616
  62. multipers/gudhi/gudhi/Persistence_matrix/columns/chain_column_extra_properties.h +150 -150
  63. multipers/gudhi/gudhi/Persistence_matrix/columns/column_dimension_holder.h +106 -106
  64. multipers/gudhi/gudhi/Persistence_matrix/columns/column_utilities.h +219 -219
  65. multipers/gudhi/gudhi/Persistence_matrix/columns/entry_types.h +327 -327
  66. multipers/gudhi/gudhi/Persistence_matrix/columns/heap_column.h +1140 -1140
  67. multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_list_column.h +934 -934
  68. multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_set_column.h +934 -934
  69. multipers/gudhi/gudhi/Persistence_matrix/columns/list_column.h +980 -980
  70. multipers/gudhi/gudhi/Persistence_matrix/columns/naive_vector_column.h +1092 -1092
  71. multipers/gudhi/gudhi/Persistence_matrix/columns/row_access.h +192 -192
  72. multipers/gudhi/gudhi/Persistence_matrix/columns/set_column.h +921 -921
  73. multipers/gudhi/gudhi/Persistence_matrix/columns/small_vector_column.h +1093 -1093
  74. multipers/gudhi/gudhi/Persistence_matrix/columns/unordered_set_column.h +1012 -1012
  75. multipers/gudhi/gudhi/Persistence_matrix/columns/vector_column.h +1244 -1244
  76. multipers/gudhi/gudhi/Persistence_matrix/matrix_dimension_holders.h +186 -186
  77. multipers/gudhi/gudhi/Persistence_matrix/matrix_row_access.h +164 -164
  78. multipers/gudhi/gudhi/Persistence_matrix/ru_pairing.h +156 -156
  79. multipers/gudhi/gudhi/Persistence_matrix/ru_rep_cycles.h +376 -376
  80. multipers/gudhi/gudhi/Persistence_matrix/ru_vine_swap.h +540 -540
  81. multipers/gudhi/gudhi/Persistent_cohomology/Field_Zp.h +118 -118
  82. multipers/gudhi/gudhi/Persistent_cohomology/Multi_field.h +173 -173
  83. multipers/gudhi/gudhi/Persistent_cohomology/Persistent_cohomology_column.h +128 -128
  84. multipers/gudhi/gudhi/Persistent_cohomology.h +745 -745
  85. multipers/gudhi/gudhi/Points_off_io.h +171 -171
  86. multipers/gudhi/gudhi/Simple_object_pool.h +69 -69
  87. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_iterators.h +463 -463
  88. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h +83 -83
  89. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_siblings.h +106 -106
  90. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_star_simplex_iterators.h +277 -277
  91. multipers/gudhi/gudhi/Simplex_tree/hooks_simplex_base.h +62 -62
  92. multipers/gudhi/gudhi/Simplex_tree/indexing_tag.h +27 -27
  93. multipers/gudhi/gudhi/Simplex_tree/serialization_utils.h +62 -62
  94. multipers/gudhi/gudhi/Simplex_tree/simplex_tree_options.h +157 -157
  95. multipers/gudhi/gudhi/Simplex_tree.h +2794 -2794
  96. multipers/gudhi/gudhi/Simplex_tree_multi.h +152 -163
  97. multipers/gudhi/gudhi/distance_functions.h +62 -62
  98. multipers/gudhi/gudhi/graph_simplicial_complex.h +104 -104
  99. multipers/gudhi/gudhi/persistence_interval.h +253 -253
  100. multipers/gudhi/gudhi/persistence_matrix_options.h +170 -170
  101. multipers/gudhi/gudhi/reader_utils.h +367 -367
  102. multipers/gudhi/mma_interface_coh.h +256 -255
  103. multipers/gudhi/mma_interface_h0.h +223 -231
  104. multipers/gudhi/mma_interface_matrix.h +291 -282
  105. multipers/gudhi/naive_merge_tree.h +536 -575
  106. multipers/gudhi/scc_io.h +310 -289
  107. multipers/gudhi/truc.h +957 -888
  108. multipers/io.cp312-win_amd64.pyd +0 -0
  109. multipers/io.pyx +714 -711
  110. multipers/ml/accuracies.py +90 -90
  111. multipers/ml/invariants_with_persistable.py +79 -79
  112. multipers/ml/kernels.py +176 -176
  113. multipers/ml/mma.py +713 -714
  114. multipers/ml/one.py +472 -472
  115. multipers/ml/point_clouds.py +352 -346
  116. multipers/ml/signed_measures.py +1589 -1589
  117. multipers/ml/sliced_wasserstein.py +461 -461
  118. multipers/ml/tools.py +113 -113
  119. multipers/mma_structures.cp312-win_amd64.pyd +0 -0
  120. multipers/mma_structures.pxd +127 -127
  121. multipers/mma_structures.pyx +4 -8
  122. multipers/mma_structures.pyx.tp +1083 -1085
  123. multipers/multi_parameter_rank_invariant/diff_helpers.h +84 -93
  124. multipers/multi_parameter_rank_invariant/euler_characteristic.h +97 -97
  125. multipers/multi_parameter_rank_invariant/function_rips.h +322 -322
  126. multipers/multi_parameter_rank_invariant/hilbert_function.h +769 -769
  127. multipers/multi_parameter_rank_invariant/persistence_slices.h +148 -148
  128. multipers/multi_parameter_rank_invariant/rank_invariant.h +369 -369
  129. multipers/multiparameter_edge_collapse.py +41 -41
  130. multipers/multiparameter_module_approximation/approximation.h +2298 -2295
  131. multipers/multiparameter_module_approximation/combinatory.h +129 -129
  132. multipers/multiparameter_module_approximation/debug.h +107 -107
  133. multipers/multiparameter_module_approximation/format_python-cpp.h +286 -286
  134. multipers/multiparameter_module_approximation/heap_column.h +238 -238
  135. multipers/multiparameter_module_approximation/images.h +79 -79
  136. multipers/multiparameter_module_approximation/list_column.h +174 -174
  137. multipers/multiparameter_module_approximation/list_column_2.h +232 -232
  138. multipers/multiparameter_module_approximation/ru_matrix.h +347 -347
  139. multipers/multiparameter_module_approximation/set_column.h +135 -135
  140. multipers/multiparameter_module_approximation/structure_higher_dim_barcode.h +36 -36
  141. multipers/multiparameter_module_approximation/unordered_set_column.h +166 -166
  142. multipers/multiparameter_module_approximation/utilities.h +403 -419
  143. multipers/multiparameter_module_approximation/vector_column.h +223 -223
  144. multipers/multiparameter_module_approximation/vector_matrix.h +331 -331
  145. multipers/multiparameter_module_approximation/vineyards.h +464 -464
  146. multipers/multiparameter_module_approximation/vineyards_trajectories.h +649 -649
  147. multipers/multiparameter_module_approximation.cp312-win_amd64.pyd +0 -0
  148. multipers/multiparameter_module_approximation.pyx +218 -217
  149. multipers/pickle.py +90 -53
  150. multipers/plots.py +342 -334
  151. multipers/point_measure.cp312-win_amd64.pyd +0 -0
  152. multipers/point_measure.pyx +322 -320
  153. multipers/simplex_tree_multi.cp312-win_amd64.pyd +0 -0
  154. multipers/simplex_tree_multi.pxd +133 -133
  155. multipers/simplex_tree_multi.pyx +115 -48
  156. multipers/simplex_tree_multi.pyx.tp +1947 -1935
  157. multipers/slicer.cp312-win_amd64.pyd +0 -0
  158. multipers/slicer.pxd +281 -100
  159. multipers/slicer.pxd.tp +218 -214
  160. multipers/slicer.pyx +1570 -507
  161. multipers/slicer.pyx.tp +931 -914
  162. multipers/tensor/tensor.h +672 -672
  163. multipers/tensor.pxd +13 -13
  164. multipers/test.pyx +44 -44
  165. multipers/tests/__init__.py +57 -57
  166. multipers/torch/diff_grids.py +217 -217
  167. multipers/torch/rips_density.py +310 -304
  168. {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/LICENSE +21 -21
  169. {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/METADATA +21 -11
  170. multipers-2.3.1.dist-info/RECORD +182 -0
  171. {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/WHEEL +1 -1
  172. multipers/tests/test_diff_helper.py +0 -73
  173. multipers/tests/test_hilbert_function.py +0 -82
  174. multipers/tests/test_mma.py +0 -83
  175. multipers/tests/test_point_clouds.py +0 -49
  176. multipers/tests/test_python-cpp_conversion.py +0 -82
  177. multipers/tests/test_signed_betti.py +0 -181
  178. multipers/tests/test_signed_measure.py +0 -89
  179. multipers/tests/test_simplextreemulti.py +0 -221
  180. multipers/tests/test_slicer.py +0 -221
  181. multipers-2.2.3.dist-info/RECORD +0 -189
  182. {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/top_level.txt +0 -0
@@ -1,164 +1,164 @@
1
- /* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
2
- * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
3
- * Author(s): Hannah Schreiber
4
- *
5
- * Copyright (C) 2022-24 Inria
6
- *
7
- * Modification(s):
8
- * - YYYY/MM Author: Description of the modification
9
- */
10
-
11
- /**
12
- * @file matrix_row_access.h
13
- * @author Hannah Schreiber
14
- * @brief Contains the @ref Gudhi::persistence_matrix::Matrix_row_access class and
15
- * @ref Gudhi::persistence_matrix::Dummy_matrix_row_access structure.
16
- */
17
-
18
- #ifndef PM_BASE_MATRIX_RA_H
19
- #define PM_BASE_MATRIX_RA_H
20
-
21
- #include <utility> //std::move
22
-
23
- namespace Gudhi {
24
- namespace persistence_matrix {
25
-
26
- /**
27
- * @ingroup persistence_matrix
28
- *
29
- * @brief Empty structure.
30
- * Inherited instead of @ref Matrix_row_access, when the the row access is not enabled.
31
- */
32
- struct Dummy_matrix_row_access
33
- {
34
- Dummy_matrix_row_access([[maybe_unused]] unsigned int numberOfRows = 0){};
35
-
36
- friend void swap([[maybe_unused]] Dummy_matrix_row_access& d1, [[maybe_unused]] Dummy_matrix_row_access& d2) {}
37
- };
38
-
39
- /**
40
- * @class Matrix_row_access matrix_row_access.h gudhi/Persistence_matrix/matrix_row_access.h
41
- * @ingroup persistence_matrix
42
- *
43
- * @brief Class managing the row access for the inheriting matrix.
44
- *
45
- * @tparam Row Either boost::intrusive::list<Matrix_entry,...> if @ref PersistenceMatrixOptions::has_intrusive_rows
46
- * is true, or std::set<Matrix_entry, RowEntryComp> otherwise.
47
- * @tparam Row_container Either std::map<Index,Row> if @ref PersistenceMatrixOptions::has_removable_rows is
48
- * true, or std::vector<Row> otherwise.
49
- * @tparam has_removable_rows Value of @ref PersistenceMatrixOptions::has_removable_rows.
50
- * @tparam ID_index @ref IDIdx index type.
51
- */
52
- template <typename Row, typename Row_container, bool has_removable_rows, typename ID_index>
53
- class Matrix_row_access
54
- {
55
- public:
56
- /**
57
- * @brief Default constructor.
58
- */
59
- Matrix_row_access() : rows_(new Row_container()){};
60
- /**
61
- * @brief Constructor reserving space for the given number of rows.
62
- *
63
- * Has only an effect if @ref PersistenceMatrixOptions::has_removable_rows is false.
64
- *
65
- * @param numberOfRows Number of rows to reserve space for.
66
- */
67
- Matrix_row_access(unsigned int numberOfRows) : rows_(new Row_container()) {
68
- if constexpr (!has_removable_rows) {
69
- rows_->resize(numberOfRows);
70
- }
71
- }
72
- /**
73
- * @brief Copy constructor.
74
- *
75
- * @param toCopy Matrix to copy.
76
- */
77
- Matrix_row_access(const Matrix_row_access& toCopy)
78
- : rows_(new Row_container()) // as the matrix is rebuild, the rows should not be copied.
79
- {
80
- if constexpr (!has_removable_rows) {
81
- rows_->resize(toCopy.rows_->size());
82
- }
83
- }
84
- /**
85
- * @brief Move constructor.
86
- *
87
- * @param other Matrix to move.
88
- */
89
- Matrix_row_access(Matrix_row_access&& other) noexcept : rows_(std::exchange(other.rows_, nullptr)) {}
90
- /**
91
- * @brief Destructor.
92
- */
93
- ~Matrix_row_access() { delete rows_; }
94
-
95
- /**
96
- * @brief Returns the row at the given @ref rowindex "row index".
97
- * The type of the row depends on the choosen options, see @ref PersistenceMatrixOptions::has_intrusive_rows.
98
- *
99
- * @param rowIndex @ref rowindex "Row index" of the row to return: @ref IDIdx for @ref chainmatrix "chain matrices"
100
- * or updated @ref IDIdx for @ref boundarymatrix "boundary matrices" if swaps occurred.
101
- * @return Reference to the row.
102
- */
103
- Row& get_row(ID_index rowIndex) {
104
- if constexpr (has_removable_rows) {
105
- return rows_->at(rowIndex);
106
- } else {
107
- return rows_->operator[](rowIndex);
108
- }
109
- }
110
- /**
111
- * @brief Returns the row at the given @ref rowindex "row index".
112
- * The type of the row depends on the choosen options, see @ref PersistenceMatrixOptions::has_intrusive_rows.
113
- *
114
- * @param rowIndex @ref rowindex "Row index" of the row to return: @ref IDIdx for @ref chainmatrix "chain matrices"
115
- * or updated @ref IDIdx for @ref boundarymatrix "boundary matrices" if swaps occurred.
116
- * @return Const reference to the row.
117
- */
118
- const Row& get_row(ID_index rowIndex) const {
119
- if constexpr (has_removable_rows) {
120
- return rows_->at(rowIndex);
121
- } else {
122
- return rows_->operator[](rowIndex);
123
- }
124
- }
125
- /**
126
- * @brief Only available if @ref PersistenceMatrixOptions::has_removable_rows is true. Removes the given row
127
- * from the row container if the row exists and is empty.
128
- *
129
- * @param rowIndex @ref rowindex "Row index" of the row to remove.
130
- */
131
- void erase_empty_row(ID_index rowIndex) {
132
- static_assert(has_removable_rows, "'erase_empty_row' is not implemented for the chosen options.");
133
-
134
- auto it = rows_->find(rowIndex);
135
- if (it != rows_->end() && it->second.empty()) rows_->erase(it);
136
- }
137
-
138
- /**
139
- * @brief Assign operator.
140
- */
141
- Matrix_row_access& operator=(const Matrix_row_access& other) {
142
- if constexpr (has_removable_rows)
143
- rows_->reserve(other.rows_->size());
144
- else
145
- rows_->resize(other.rows_->size());
146
- return *this;
147
- }
148
- /**
149
- * @brief Swap operator.
150
- */
151
- friend void swap(Matrix_row_access& matrix1, Matrix_row_access& matrix2) { std::swap(matrix1.rows_, matrix2.rows_); }
152
-
153
- protected:
154
- /**
155
- * @brief Row container. A pointer to facilitate column swaps when two matrices are swapped.
156
- * Has to be destroyed after matrix_, therefore has to be inherited.
157
- */
158
- Row_container* rows_;
159
- };
160
-
161
- } // namespace persistence_matrix
162
- } // namespace Gudhi
163
-
164
- #endif // PM_BASE_MATRIX_RA_H
1
+ /* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
2
+ * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
3
+ * Author(s): Hannah Schreiber
4
+ *
5
+ * Copyright (C) 2022-24 Inria
6
+ *
7
+ * Modification(s):
8
+ * - YYYY/MM Author: Description of the modification
9
+ */
10
+
11
+ /**
12
+ * @file matrix_row_access.h
13
+ * @author Hannah Schreiber
14
+ * @brief Contains the @ref Gudhi::persistence_matrix::Matrix_row_access class and
15
+ * @ref Gudhi::persistence_matrix::Dummy_matrix_row_access structure.
16
+ */
17
+
18
+ #ifndef PM_BASE_MATRIX_RA_H
19
+ #define PM_BASE_MATRIX_RA_H
20
+
21
+ #include <utility> //std::move
22
+
23
+ namespace Gudhi {
24
+ namespace persistence_matrix {
25
+
26
+ /**
27
+ * @ingroup persistence_matrix
28
+ *
29
+ * @brief Empty structure.
30
+ * Inherited instead of @ref Matrix_row_access, when the the row access is not enabled.
31
+ */
32
+ struct Dummy_matrix_row_access
33
+ {
34
+ Dummy_matrix_row_access([[maybe_unused]] unsigned int numberOfRows = 0){};
35
+
36
+ friend void swap([[maybe_unused]] Dummy_matrix_row_access& d1, [[maybe_unused]] Dummy_matrix_row_access& d2) {}
37
+ };
38
+
39
+ /**
40
+ * @class Matrix_row_access matrix_row_access.h gudhi/Persistence_matrix/matrix_row_access.h
41
+ * @ingroup persistence_matrix
42
+ *
43
+ * @brief Class managing the row access for the inheriting matrix.
44
+ *
45
+ * @tparam Row Either boost::intrusive::list<Matrix_entry,...> if @ref PersistenceMatrixOptions::has_intrusive_rows
46
+ * is true, or std::set<Matrix_entry, RowEntryComp> otherwise.
47
+ * @tparam Row_container Either std::map<Index,Row> if @ref PersistenceMatrixOptions::has_removable_rows is
48
+ * true, or std::vector<Row> otherwise.
49
+ * @tparam has_removable_rows Value of @ref PersistenceMatrixOptions::has_removable_rows.
50
+ * @tparam ID_index @ref IDIdx index type.
51
+ */
52
+ template <typename Row, typename Row_container, bool has_removable_rows, typename ID_index>
53
+ class Matrix_row_access
54
+ {
55
+ public:
56
+ /**
57
+ * @brief Default constructor.
58
+ */
59
+ Matrix_row_access() : rows_(new Row_container()){};
60
+ /**
61
+ * @brief Constructor reserving space for the given number of rows.
62
+ *
63
+ * Has only an effect if @ref PersistenceMatrixOptions::has_removable_rows is false.
64
+ *
65
+ * @param numberOfRows Number of rows to reserve space for.
66
+ */
67
+ Matrix_row_access(unsigned int numberOfRows) : rows_(new Row_container()) {
68
+ if constexpr (!has_removable_rows) {
69
+ rows_->resize(numberOfRows);
70
+ }
71
+ }
72
+ /**
73
+ * @brief Copy constructor.
74
+ *
75
+ * @param toCopy Matrix to copy.
76
+ */
77
+ Matrix_row_access(const Matrix_row_access& toCopy)
78
+ : rows_(new Row_container()) // as the matrix is rebuild, the rows should not be copied.
79
+ {
80
+ if constexpr (!has_removable_rows) {
81
+ rows_->resize(toCopy.rows_->size());
82
+ }
83
+ }
84
+ /**
85
+ * @brief Move constructor.
86
+ *
87
+ * @param other Matrix to move.
88
+ */
89
+ Matrix_row_access(Matrix_row_access&& other) noexcept : rows_(std::exchange(other.rows_, nullptr)) {}
90
+ /**
91
+ * @brief Destructor.
92
+ */
93
+ ~Matrix_row_access() { delete rows_; }
94
+
95
+ /**
96
+ * @brief Returns the row at the given @ref rowindex "row index".
97
+ * The type of the row depends on the choosen options, see @ref PersistenceMatrixOptions::has_intrusive_rows.
98
+ *
99
+ * @param rowIndex @ref rowindex "Row index" of the row to return: @ref IDIdx for @ref chainmatrix "chain matrices"
100
+ * or updated @ref IDIdx for @ref boundarymatrix "boundary matrices" if swaps occurred.
101
+ * @return Reference to the row.
102
+ */
103
+ Row& get_row(ID_index rowIndex) {
104
+ if constexpr (has_removable_rows) {
105
+ return rows_->at(rowIndex);
106
+ } else {
107
+ return rows_->operator[](rowIndex);
108
+ }
109
+ }
110
+ /**
111
+ * @brief Returns the row at the given @ref rowindex "row index".
112
+ * The type of the row depends on the choosen options, see @ref PersistenceMatrixOptions::has_intrusive_rows.
113
+ *
114
+ * @param rowIndex @ref rowindex "Row index" of the row to return: @ref IDIdx for @ref chainmatrix "chain matrices"
115
+ * or updated @ref IDIdx for @ref boundarymatrix "boundary matrices" if swaps occurred.
116
+ * @return Const reference to the row.
117
+ */
118
+ const Row& get_row(ID_index rowIndex) const {
119
+ if constexpr (has_removable_rows) {
120
+ return rows_->at(rowIndex);
121
+ } else {
122
+ return rows_->operator[](rowIndex);
123
+ }
124
+ }
125
+ /**
126
+ * @brief Only available if @ref PersistenceMatrixOptions::has_removable_rows is true. Removes the given row
127
+ * from the row container if the row exists and is empty.
128
+ *
129
+ * @param rowIndex @ref rowindex "Row index" of the row to remove.
130
+ */
131
+ void erase_empty_row(ID_index rowIndex) {
132
+ static_assert(has_removable_rows, "'erase_empty_row' is not implemented for the chosen options.");
133
+
134
+ auto it = rows_->find(rowIndex);
135
+ if (it != rows_->end() && it->second.empty()) rows_->erase(it);
136
+ }
137
+
138
+ /**
139
+ * @brief Assign operator.
140
+ */
141
+ Matrix_row_access& operator=(const Matrix_row_access& other) {
142
+ if constexpr (has_removable_rows)
143
+ rows_->reserve(other.rows_->size());
144
+ else
145
+ rows_->resize(other.rows_->size());
146
+ return *this;
147
+ }
148
+ /**
149
+ * @brief Swap operator.
150
+ */
151
+ friend void swap(Matrix_row_access& matrix1, Matrix_row_access& matrix2) { std::swap(matrix1.rows_, matrix2.rows_); }
152
+
153
+ protected:
154
+ /**
155
+ * @brief Row container. A pointer to facilitate column swaps when two matrices are swapped.
156
+ * Has to be destroyed after matrix_, therefore has to be inherited.
157
+ */
158
+ Row_container* rows_;
159
+ };
160
+
161
+ } // namespace persistence_matrix
162
+ } // namespace Gudhi
163
+
164
+ #endif // PM_BASE_MATRIX_RA_H
@@ -1,156 +1,156 @@
1
- /* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
2
- * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
3
- * Author(s): Hannah Schreiber
4
- *
5
- * Copyright (C) 2022-24 Inria
6
- *
7
- * Modification(s):
8
- * - YYYY/MM Author: Description of the modification
9
- */
10
-
11
- /**
12
- * @file ru_pairing.h
13
- * @author Hannah Schreiber
14
- * @brief Contains the @ref Gudhi::persistence_matrix::RU_pairing class and
15
- * @ref Gudhi::persistence_matrix::Dummy_ru_pairing structure.
16
- */
17
-
18
- #ifndef PM_RU_PAIRING_H
19
- #define PM_RU_PAIRING_H
20
-
21
- #include <unordered_map>
22
-
23
- #include "boundary_cell_position_to_id_mapper.h"
24
-
25
- namespace Gudhi {
26
- namespace persistence_matrix {
27
-
28
- /**
29
- * @ingroup persistence_matrix
30
- *
31
- * @brief Empty structure.
32
- * Inherited instead of @ref RU_pairing, when the computation of the barcode was not enabled or if the pairing
33
- * is already managed by the vine update classes.
34
- */
35
- struct Dummy_ru_pairing
36
- {
37
- friend void swap([[maybe_unused]] Dummy_ru_pairing& d1, [[maybe_unused]] Dummy_ru_pairing& d2) {}
38
- };
39
-
40
- /**
41
- * @class RU_pairing ru_pairing.h gudhi/Persistence_matrix/ru_pairing.h
42
- * @ingroup persistence_matrix
43
- *
44
- * @brief Class managing the barcode for @ref RU_matrix if the option was enabled.
45
- *
46
- * @tparam Master_matrix An instantiation of @ref Matrix from which all types and options are deduced.
47
- */
48
- template <class Master_matrix>
49
- class RU_pairing : public std::conditional<
50
- Master_matrix::Option_list::has_removable_columns,
51
- Cell_position_to_ID_mapper<typename Master_matrix::ID_index, typename Master_matrix::Pos_index>,
52
- Dummy_pos_mapper
53
- >::type
54
- {
55
- protected:
56
- using Pos_index = typename Master_matrix::Pos_index;
57
- using ID_index = typename Master_matrix::ID_index;
58
- //PIDM = Position to ID Map
59
- using PIDM = typename std::conditional<Master_matrix::Option_list::has_removable_columns,
60
- Cell_position_to_ID_mapper<ID_index, Pos_index>,
61
- Dummy_pos_mapper
62
- >::type;
63
-
64
- public:
65
- using Barcode = typename Master_matrix::Barcode; /**< Barcode type. */
66
-
67
- /**
68
- * @brief Default constructor.
69
- */
70
- RU_pairing() : PIDM() {}
71
-
72
- /**
73
- * @brief Returns the current barcode which is maintained at any insertion, removal or vine swap.
74
- *
75
- * @return Const reference to the barcode.
76
- */
77
- const Barcode& get_current_barcode() const { return barcode_; }
78
-
79
- /**
80
- * @brief Swap operator.
81
- */
82
- friend void swap(RU_pairing& pairing1, RU_pairing& pairing2) {
83
- swap(static_cast<PIDM&>(pairing1), static_cast<PIDM&>(pairing2));
84
- pairing1.barcode_.swap(pairing2.barcode_);
85
- pairing1.indexToBar_.swap(pairing2.indexToBar_);
86
- pairing1.idToPosition_.swap(pairing2.idToPosition_);
87
- }
88
-
89
- protected:
90
- using Dimension = typename Master_matrix::Dimension;
91
- using Dictionary = typename Master_matrix::Bar_dictionary;
92
-
93
- Barcode barcode_; /**< Bar container. */
94
- Dictionary indexToBar_; /**< Map from @ref MatIdx index to bar index. */
95
- /**
96
- * @brief Map from cell ID to cell position. Only stores a pair if ID != position.
97
- */
98
- std::unordered_map<ID_index, Pos_index> idToPosition_; //TODO: test other map types
99
-
100
- void _update_barcode(ID_index birthPivot, Pos_index death) {
101
- auto it = idToPosition_.find(birthPivot);
102
- Pos_index pivotBirth = it == idToPosition_.end() ? birthPivot : it->second;
103
- if constexpr (Master_matrix::hasFixedBarcode || !Master_matrix::Option_list::has_removable_columns) {
104
- barcode_[indexToBar_[pivotBirth]].death = death;
105
- indexToBar_.push_back(indexToBar_[pivotBirth]);
106
- } else {
107
- auto& barIt = indexToBar_.at(pivotBirth);
108
- barIt->death = death;
109
- indexToBar_.try_emplace(death, barIt); // list so iterators are stable
110
- }
111
- }
112
-
113
- void _add_bar(Dimension dim, Pos_index birth) {
114
- barcode_.emplace_back(birth, -1, dim);
115
- if constexpr (Master_matrix::hasFixedBarcode || !Master_matrix::Option_list::has_removable_columns) {
116
- indexToBar_.push_back(barcode_.size() - 1);
117
- } else {
118
- indexToBar_.try_emplace(birth, --barcode_.end());
119
- }
120
- }
121
-
122
- void _remove_last(Pos_index eventIndex) {
123
- static_assert(Master_matrix::Option_list::has_removable_columns, "_remove_last not available.");
124
-
125
- if constexpr (Master_matrix::hasFixedBarcode) {
126
- auto& bar = barcode_[indexToBar_[eventIndex]];
127
- if (bar.death == static_cast<Pos_index>(-1)) { // birth
128
- barcode_.pop_back(); // sorted by birth and eventIndex has to be the highest one
129
- } else { // death
130
- bar.death = -1;
131
- };
132
- indexToBar_.pop_back();
133
- } else { // birth order eventually shuffled by vine updates. No sort possible to keep the matchings.
134
- auto it = indexToBar_.find(eventIndex);
135
- typename Barcode::iterator bar = it->second;
136
-
137
- if (bar->death == static_cast<Pos_index>(-1))
138
- barcode_.erase(bar);
139
- else
140
- bar->death = -1;
141
-
142
- indexToBar_.erase(it);
143
- }
144
-
145
- auto it = PIDM::map_.find(eventIndex);
146
- if (it != PIDM::map_.end()){
147
- idToPosition_.erase(it->second);
148
- PIDM::map_.erase(it);
149
- }
150
- }
151
- };
152
-
153
- } // namespace persistence_matrix
154
- } // namespace Gudhi
155
-
156
- #endif // PM_RU_PAIRING_H
1
+ /* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
2
+ * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
3
+ * Author(s): Hannah Schreiber
4
+ *
5
+ * Copyright (C) 2022-24 Inria
6
+ *
7
+ * Modification(s):
8
+ * - YYYY/MM Author: Description of the modification
9
+ */
10
+
11
+ /**
12
+ * @file ru_pairing.h
13
+ * @author Hannah Schreiber
14
+ * @brief Contains the @ref Gudhi::persistence_matrix::RU_pairing class and
15
+ * @ref Gudhi::persistence_matrix::Dummy_ru_pairing structure.
16
+ */
17
+
18
+ #ifndef PM_RU_PAIRING_H
19
+ #define PM_RU_PAIRING_H
20
+
21
+ #include <unordered_map>
22
+
23
+ #include "boundary_cell_position_to_id_mapper.h"
24
+
25
+ namespace Gudhi {
26
+ namespace persistence_matrix {
27
+
28
+ /**
29
+ * @ingroup persistence_matrix
30
+ *
31
+ * @brief Empty structure.
32
+ * Inherited instead of @ref RU_pairing, when the computation of the barcode was not enabled or if the pairing
33
+ * is already managed by the vine update classes.
34
+ */
35
+ struct Dummy_ru_pairing
36
+ {
37
+ friend void swap([[maybe_unused]] Dummy_ru_pairing& d1, [[maybe_unused]] Dummy_ru_pairing& d2) {}
38
+ };
39
+
40
+ /**
41
+ * @class RU_pairing ru_pairing.h gudhi/Persistence_matrix/ru_pairing.h
42
+ * @ingroup persistence_matrix
43
+ *
44
+ * @brief Class managing the barcode for @ref RU_matrix if the option was enabled.
45
+ *
46
+ * @tparam Master_matrix An instantiation of @ref Matrix from which all types and options are deduced.
47
+ */
48
+ template <class Master_matrix>
49
+ class RU_pairing : public std::conditional<
50
+ Master_matrix::Option_list::has_removable_columns,
51
+ Cell_position_to_ID_mapper<typename Master_matrix::ID_index, typename Master_matrix::Pos_index>,
52
+ Dummy_pos_mapper
53
+ >::type
54
+ {
55
+ protected:
56
+ using Pos_index = typename Master_matrix::Pos_index;
57
+ using ID_index = typename Master_matrix::ID_index;
58
+ //PIDM = Position to ID Map
59
+ using PIDM = typename std::conditional<Master_matrix::Option_list::has_removable_columns,
60
+ Cell_position_to_ID_mapper<ID_index, Pos_index>,
61
+ Dummy_pos_mapper
62
+ >::type;
63
+
64
+ public:
65
+ using Barcode = typename Master_matrix::Barcode; /**< Barcode type. */
66
+
67
+ /**
68
+ * @brief Default constructor.
69
+ */
70
+ RU_pairing() : PIDM() {}
71
+
72
+ /**
73
+ * @brief Returns the current barcode which is maintained at any insertion, removal or vine swap.
74
+ *
75
+ * @return Const reference to the barcode.
76
+ */
77
+ const Barcode& get_current_barcode() const { return barcode_; }
78
+
79
+ /**
80
+ * @brief Swap operator.
81
+ */
82
+ friend void swap(RU_pairing& pairing1, RU_pairing& pairing2) {
83
+ swap(static_cast<PIDM&>(pairing1), static_cast<PIDM&>(pairing2));
84
+ pairing1.barcode_.swap(pairing2.barcode_);
85
+ pairing1.indexToBar_.swap(pairing2.indexToBar_);
86
+ pairing1.idToPosition_.swap(pairing2.idToPosition_);
87
+ }
88
+
89
+ protected:
90
+ using Dimension = typename Master_matrix::Dimension;
91
+ using Dictionary = typename Master_matrix::Bar_dictionary;
92
+
93
+ Barcode barcode_; /**< Bar container. */
94
+ Dictionary indexToBar_; /**< Map from @ref MatIdx index to bar index. */
95
+ /**
96
+ * @brief Map from cell ID to cell position. Only stores a pair if ID != position.
97
+ */
98
+ std::unordered_map<ID_index, Pos_index> idToPosition_; //TODO: test other map types
99
+
100
+ void _update_barcode(ID_index birthPivot, Pos_index death) {
101
+ auto it = idToPosition_.find(birthPivot);
102
+ Pos_index pivotBirth = it == idToPosition_.end() ? birthPivot : it->second;
103
+ if constexpr (Master_matrix::hasFixedBarcode || !Master_matrix::Option_list::has_removable_columns) {
104
+ barcode_[indexToBar_[pivotBirth]].death = death;
105
+ indexToBar_.push_back(indexToBar_[pivotBirth]);
106
+ } else {
107
+ auto& barIt = indexToBar_.at(pivotBirth);
108
+ barIt->death = death;
109
+ indexToBar_.try_emplace(death, barIt); // list so iterators are stable
110
+ }
111
+ }
112
+
113
+ void _add_bar(Dimension dim, Pos_index birth) {
114
+ barcode_.emplace_back(birth, -1, dim);
115
+ if constexpr (Master_matrix::hasFixedBarcode || !Master_matrix::Option_list::has_removable_columns) {
116
+ indexToBar_.push_back(barcode_.size() - 1);
117
+ } else {
118
+ indexToBar_.try_emplace(birth, --barcode_.end());
119
+ }
120
+ }
121
+
122
+ void _remove_last(Pos_index eventIndex) {
123
+ static_assert(Master_matrix::Option_list::has_removable_columns, "_remove_last not available.");
124
+
125
+ if constexpr (Master_matrix::hasFixedBarcode) {
126
+ auto& bar = barcode_[indexToBar_[eventIndex]];
127
+ if (bar.death == static_cast<Pos_index>(-1)) { // birth
128
+ barcode_.pop_back(); // sorted by birth and eventIndex has to be the highest one
129
+ } else { // death
130
+ bar.death = -1;
131
+ };
132
+ indexToBar_.pop_back();
133
+ } else { // birth order eventually shuffled by vine updates. No sort possible to keep the matchings.
134
+ auto it = indexToBar_.find(eventIndex);
135
+ typename Barcode::iterator bar = it->second;
136
+
137
+ if (bar->death == static_cast<Pos_index>(-1))
138
+ barcode_.erase(bar);
139
+ else
140
+ bar->death = -1;
141
+
142
+ indexToBar_.erase(it);
143
+ }
144
+
145
+ auto it = PIDM::map_.find(eventIndex);
146
+ if (it != PIDM::map_.end()){
147
+ idToPosition_.erase(it->second);
148
+ PIDM::map_.erase(it);
149
+ }
150
+ }
151
+ };
152
+
153
+ } // namespace persistence_matrix
154
+ } // namespace Gudhi
155
+
156
+ #endif // PM_RU_PAIRING_H